<p>Skilled movement relies on descending cortical projections to the brainstem and spinal cord. The brainstem integrates cortical inputs from subcerebral projection neurons (SCPN). Here, we identify a previously unrecognized direct cortico-brainstem circuit that emerges early in development and persists into adulthood. A subset of SCPN project exclusively to the brainstem from the earliest stages of axon extension, never extending to the spinal cord. We find that during development, these cortico-brainstem neurons (CBN) can be prospectively identified by Neuropeptide Y (Npy) expression. In adulthood, Npy⁺ CBN project preferentially to rostral brainstem motor regions. Silencing Npy⁺ CBN impairs the precision and targeting of forelimb movement in a skilled reaching task. Together, these results outline how molecular programs lay the foundation for adult cortico-brainstem circuits underlying skilled movement. Our findings reveal the developmental logic diversifying descending cortical circuits and enable investigation of specific descending projection neuron subsets in motor control.</p>